Z-Form Adoption of Nucleic Acid is a Multi-Step Process Which Proceeds through a Melted Intermediate
Z-Form Adoption of Nucleic Acid is a Multi-Step Process Which Proceeds through a Melted Intermediate
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DOI：
10.1021/jacs.3c10406
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发表时间：
2023-12-22
影响因子：
15
通讯作者：
Vogeli，Beat
中科院分区：
文献类型：
--
作者：
Nichols，Parker J.;Krall，Jeffrey B.;Vogeli，Beat
核酸的左手Z-构象可以被DNA和RNA采用，当被在各种先天免疫应答蛋白中发现的Zα结构域结合时。Zα结构域通过与Z-DNA/Z-RNA的独特几何结构发生特异性相互作用来稳定这种高能构象。然而，在蛋白质的存在下，右旋螺旋扭曲成左旋的机制，包括所涉及的中间步骤，知之甚少。通过核磁共振（NMR）和其他生物物理测量的组合，我们已经确定，在不存在Zα的情况下，在室温低盐条件下，d（CpG）和r（CpG）构建体在中间或慢NMR时间尺度上均未显示出大于0.5%的瞬时Z构象的可观察证据。在较高的温度下，我们观察到一个短暂的未折叠的中间体。核酸双链体解链的难易程度与Zα存在下的Z型采用率相关。通过Arrhenius图计算的Z-形式采用的活化能的最大贡献因素是翻转糖褶皱的容易性，如Z-DNA和Z-RNA所需。总之，这些数据验证了先前提出的Z形采用Zα的“拉链模型”。总的来说，Z-构象更可能被双链DNA和RNA区域采用，所述双链DNA和RNA区域两侧是不太稳定的区域和经历扭转/机械应力的RNA。
The left-handed Z-conformation of nucleic acids can be adopted by both DNA and RNA when bound by Zα domains found within a variety of innate immune response proteins. Zα domains stabilize this higher-energy conformation by making specific interactions with the unique geometry of Z-DNA/Z-RNA. However, the mechanism by which a right-handed helix contorts to become left-handed in the presence of proteins, including the intermediate steps involved, is poorly understood. Through a combination of nuclear magnetic resonance (NMR) and other biophysical measurements, we have determined that in the absence of Zα, under low salt conditions at room temperature, d(CpG) and r(CpG) constructs show no observable evidence of transient Z-conformations greater than 0.5% on either the intermediate or slow NMR time scales. At higher temperatures, we observed a transient unfolded intermediate. The ease of melting a nucleic acid duplex correlates with Z-form adoption rates in the presence of Zα. The largest contributing factor to the activation energies of Z-form adoption as calculated by Arrhenius plots is the ease of flipping the sugar pucker, as required for Z-DNA and Z-RNA. Together, these data validate the previously proposed “zipper model” for Z-form adoption in the presence of Zα. Overall, Z-conformations are more likely to be adopted by double-stranded DNA and RNA regions flanked by less stable regions and by RNAs experiencing torsional/mechanical stress.